Consensus Sequence Generator For Cloning

Question

[JW]

I've finished cloning a cDNA into a vector and obtained various sequence files from forward and reverse primers. I would like to combine them together to form a consensus sequence and be able to view the different reads from my different files (something like the Lasergene software but open source). What is a good program to use?

Answer 1

[Josh Herr]

I would break your question down into two parts, both of which are fairly common around here.

There are numerous tools to generate consensus sequences: Multiple Sequence Alignment Editor With Option To Generate Consensus Sequence and here also. I have used this consensus tool before with success.

I use primer3 to design primers. Make sure you understand all the parameters when designing primers; just speaking from my own experience here.